This way should be quicker, take less steps. This version it for systems capable of bitstreaming. For those who don't know what bitstreaming it; it is outputting straight uncompressed audio over HDMI to your receiver. In the forms of Dolby TrueHD, DTS Master, or uncompressed PCM. If you planning on using analog sound or don't have a bistreaming capable soundcard/receiver, you will want to use the guide above for ripping the audio to FLAC. This version will also include on how to do multiple audio tracks (i.e. commentaries).

Applications needed:AnyDVD. It isn't free, actually it is kind of expensive, but very much worth it. It is pretty comparable in price to Arcsoft TMT (bluray playback software). However it is going to eliminate so many issues w/ bluray playback on a PC. mkvmerge . Free.eac3to. Free.eac3to and More GUI - There is a version included with eac3to, however I find it unbarely hard to use(maybe because it is too easy )
Arcsoft TMT. Trial works fine, as we don't ever have to run the program, just need the use its its DTS decoders. Installation instructions since we need to run an older version of this software.BDSup2Sub - used to rip subtitles and convert them to a usable format.

With this version there is no need to copy the movie to your HDD first as it really won't be all that faster. So open up eac3to. You want to make sure that the Path: Ea3to and the Destination Folder areas are correct.
Then drag and drop your bluray from My Computer in to the Sources in eac3to.
Click on the ea3to Audio tab. Then in Input File(s)or Folder drop down, select the source folder listed. There should only be one choice. Both Ea3to windows will minimize and a command window will pop up for a few seconds. Once it finishes scanning the bluray disc, the eac3to GUI windows will pop up again.
In the little Track Listings Window it now lists all the tracks on the bluray disc. Usually number 1 is the main movie. The rest will be extra features, etc. However in my case it is #2 (silly Disney put #1 as a version w/ French video).
Even the track listing (again usually #1) in to the Title Set in the main ea3to window.
eac3to will minimize for a few seconds while it scans. Now again look to the Track Listings Window. Here it will list all the tracks to the section of the bluray disc we plan on ripping. Since we are in the audio section you are looking for the audio tracks. In my case #4 is going to be the main audio track and #6 is the commentary. If there is a bunch of English audio tracks you may need to rip them all, then give each a quick listen in order to find which is the commentary you want. That is if you want commentaries at all.
Now enter the main audio track number (in my case #4)in the Track section of the main eac3to window. Then enter the name of the audio track. I just do [name of movie][audio track type]. Then select Save As Type. If the audio track is DTS-Master select dtsma. If it is a Dolby True HD then select thd. If it is AC3 select ac3. In the rare occasion that your movie has an E-AC3 audio track AND it has a bitrate higher than 640kbps then use eac3, if under 640kbps then just select ac3. Then at the bottom click Lock Current Settings To Command Line. If you don't want the commentary added skip this next step. If you plan on ripping multiple audio tracks you would now fill in the secondary audio track under Track, enter in a File Name, and Save As Type once again. Then press Lock Current Settings To Command Line again.
Now we are done with the audio section. Click on Eac3to Video tab. Refer to the Track Listings window and locate the video tracks, subtitles, and chapter tracks.
Enter the video track number (in my case #2) to the Track section of main ea3to window. Then once again fill out a File Name and Save As Type. Save as Type should be mkv. Under Chapter Tracks, select the chapters track. Then under Subtitles Track, select the English subtitle track. Then give it a name, then tab out of the space.Hit Lock Current Settings To Command Line.
The subtitle track is not needed for some movies. But almost any movie that has other languages besides English spoken in it will. If you have a movie like this you may need to rip all the subtitle tracks in order to get the one that will have subtitles for ONLY the non-English. You do this the same way we did multiple audio tracks. Select the Subtitle Track, give it a name, tab out. Then press Lock Current Settings To Command Line. Do this for every English subtitle track.

Now hit Run Command Line (Tab Specific). Eac3to will now rip the tracks we have selected from the bluray disc.This may take from 30 minutes to half an hour depending on how large the bluray movie is. After this is done you can close eac3to.You can skip the following section if you don't have any subtitles. Open up BDSup2Sub. Click File, Open. Then select the .Sup subtitle track you ripped. Click Ok. Click the lower right section.
Here you can go through all the subtitles and check if this is the one you want. The arrows at the top let you go through frame. If you want non-English subtitles only there should be only a few dozen frames in most cases. Subtitles for full movies will be 500-1500. Press Bottom because who really wants the subtitles at the top of the screen. Click OK, then File, Save/Export. Then give your subtitles a name. Then Ok. Then you can close DBSup2Sub.

Next open up mkvmerge. Next drag and drop your mkv, audio files, and IDX subtitle file in to the mkvmerge GUI window.
If you have multiple audio tracks you will need to give the tracks names to differentiate them. As well we need to set the default track. You could always name the video track but it isn't necessary. You may also want to add a language to the subtitle track.
Now click the Global tab. Then under Chapters, click Browse. Select the chapters.txt that eac3to created. Select the language. Now At the bottom select Browse under Output File Name. Name your movie. If you plan on using XBMC I highly suggest you add bluray and the audio type to the file name like I have. I will explain this under the XBMC section later on.
And we are done. You should now have a fully lossless bluray rip.